As a Vim afficiando, you might use VimWiki as a solution for storing and organizing notes, to-do lists and journal entries.
But VimWiki comes with some problems. It offers tons of features, but also heavily modifies your Vim installation. VimWiki overwrites common behavior, duplicates some functionalities, and can be hard to integrate with other plugins.
Here are some alternatives to Vimwiki:
Joe Reynolds wrote an excellent article about managing notes and to-dos without plugins.
Those methods aren't as convenient as Vimwiki. But you don't depend on a plugin.
Vim-Waikiki is a minimalist plugin for note-taking. It offers some key mappings to ease notes and link navigation.
The plugin provides a thin layer upon existing Vim features. It doesn't mess with
Vim-Waikiki is not a full replacement for Vimwiki, but it might be enough for your needs.
Wiki.Vim resembles the original Vimwiki in its feature set. No wonder, as the project was born as a fork of VimWiki.
With wiki.vim you'll get tons of key mappings for creating and navigating wiki entries. You can toggle links, create diary entries, conveniently manage to-do lists, etc.
I've found the Markdown integration less cumbersome than Vimwiki's.
Wiki.vim looks like a slimmer alternative to Vimwiki with almost the same benefits, but a lighter footprint.